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- PDB-7lhf: Structure of full-length IP3R1 channel solubilized in LNMG & lipi... -

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Basic information

Entry
Database: PDB / ID: 7lhf
TitleStructure of full-length IP3R1 channel solubilized in LNMG & lipid in the apo-state
ComponentsInositol 1,4,5-trisphosphate receptor type 1
KeywordsMEMBRANE PROTEIN / Calcium channel / lipids
Function / homology
Function and homology information


Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cGMP effects / smooth endoplasmic reticulum membrane / Elevation of cytosolic Ca2+ levels / platelet dense tubular network / calcineurin complex / platelet dense granule membrane ...Effects of PIP2 hydrolysis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / inositol 1,4,5-trisphosphate receptor activity involved in regulation of postsynaptic cytosolic calcium levels / release of sequestered calcium ion into cytosol by endoplasmic reticulum / cGMP effects / smooth endoplasmic reticulum membrane / Elevation of cytosolic Ca2+ levels / platelet dense tubular network / calcineurin complex / platelet dense granule membrane / epithelial fluid transport / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / inositol 1,4,5-trisphosphate-gated calcium channel activity / calcium import into the mitochondrion / voluntary musculoskeletal movement / inositol 1,4,5 trisphosphate binding / negative regulation of calcium-mediated signaling / positive regulation of calcium ion transport / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / endoplasmic reticulum calcium ion homeostasis / positive regulation of hepatocyte proliferation / nuclear inner membrane / Ion homeostasis / transport vesicle membrane / dendrite development / ligand-gated ion channel signaling pathway / intracellularly gated calcium channel activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / single fertilization / calcium channel inhibitor activity / GABA-ergic synapse / cellular response to cAMP / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / phosphatidylinositol binding / post-embryonic development / secretory granule membrane / sarcoplasmic reticulum / synaptic membrane / liver regeneration / cell morphogenesis / positive regulation of insulin secretion / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / calcium ion transport / nuclear envelope / presynapse / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / cellular response to hypoxia / protein phosphatase binding / protein homotetramerization / transmembrane transporter binding / postsynapse / postsynaptic density / response to hypoxia / positive regulation of apoptotic process / protein domain specific binding / neuronal cell body / calcium ion binding / dendrite / synapse / endoplasmic reticulum membrane / protein-containing complex binding / negative regulation of apoptotic process / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif ...Inositol 1,4,5-trisphosphate receptor / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / Ion transport domain / Ion transport protein / Armadillo-type fold
Similarity search - Domain/homology
Chem-PLX / Inositol 1,4,5-trisphosphate-gated calcium channel ITPR1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsBaker, M.R. / Fan, G. / Baker, M.L. / Serysheva, I.I.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM072804 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS106968 United States
Welch FoundationAU-2014-20190330 United States
American Heart Association18CDA34110086 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM063210 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY025218 United States
National Institutes of Health/National Eye Institute (NIH/NEI)R01EY026545 United States
CitationJournal: Commun Biol / Year: 2021
Title: Cryo-EM structure of type 1 IPR channel in a lipid bilayer.
Authors: Mariah R Baker / Guizhen Fan / Alexander B Seryshev / Melina A Agosto / Matthew L Baker / Irina I Serysheva /
Abstract: Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved ...Type 1 inositol 1,4,5-trisphosphate receptor (IPR1) is the predominant Ca-release channel in neurons. IPR1 mediates Ca release from the endoplasmic reticulum into the cytosol and thereby is involved in many physiological processes. Here, we present the cryo-EM structures of full-length rat IPR1 reconstituted in lipid nanodisc and detergent solubilized in the presence of phosphatidylcholine determined in ligand-free, closed states by single-particle electron cryo-microscopy. Notably, both structures exhibit the well-established IPR1 protein fold and reveal a nearly complete representation of lipids with similar locations of ordered lipids bound to the transmembrane domains. The lipid-bound structures show improved features that enabled us to unambiguously build atomic models of IPR1 including two membrane associated helices that were not previously resolved in the TM region. Our findings suggest conserved locations of protein-bound lipids among homotetrameric ion channels that are critical for their structural and functional integrity despite the diversity of structural mechanisms for their gating.
History
DepositionJan 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Data collection / Structure summary / Category: audit_author / em_image_recording / Item: _em_image_recording.film_or_detector_model
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Inositol 1,4,5-trisphosphate receptor type 1
D: Inositol 1,4,5-trisphosphate receptor type 1
B: Inositol 1,4,5-trisphosphate receptor type 1
C: Inositol 1,4,5-trisphosphate receptor type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,270,07536
Polymers1,248,3344
Non-polymers21,74132
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area61930 Å2
ΔGint-365 kcal/mol
Surface area466540 Å2

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Components

#1: Protein
Inositol 1,4,5-trisphosphate receptor type 1 / IP3 receptor isoform 1 / InsP3R1 / Type 1 inositol 1 / 4 / 5-trisphosphate receptor / Type 1 InsP3 receptor


Mass: 312083.500 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Organ: cerebellum / References: UniProt: P29994
#2: Chemical...
ChemComp-PLX / (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL


Mass: 767.132 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C42H89NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Type 1 inositol 1,4,5-trisphosphate receptor tetrameric protein complex
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 1.3 MDa / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Cellular location: membrane / Organ: cerebellum / Organelle: endoplasmic reticulum
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 46943 X / Nominal defocus min: 800 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 42 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 19105
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 3840 / Height: 3712 / Movie frames/image: 35 / Used frames/image: 2-35

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Processing

SoftwareName: PHENIX / Version: dev_svn: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
7Cootmodel fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1407714
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 303481 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6MU2

6mu2


Accession code: 6MU2 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00473240
ELECTRON MICROSCOPYf_angle_d1.01898332
ELECTRON MICROSCOPYf_dihedral_angle_d9.79110940
ELECTRON MICROSCOPYf_chiral_restr0.05511308
ELECTRON MICROSCOPYf_plane_restr0.00612104

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